HEADER OXIDOREDUCTASE 20-OCT-07 3B3E OBSLTE 25-NOV-08 3B3E 3F7J TITLE B.SUBTILIS YVGN CAVEAT 3B3E THERE ARE TWO CHIRALITY ERRORS IN CHAIN B. COMPND MOL_ID: 1; COMPND 2 MOLECULE: YVGN PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PUTATIVE REDUCTASE PROTEIN, YVGN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 GENE: YVGN; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ALDO-KETO REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.F.ZHOU,L.F.LI,Y.H.LIANG,X.-D.SU REVDAT 2 25-NOV-08 3B3E 1 OBSLTE REVDAT 1 21-OCT-08 3B3E 0 JRNL AUTH Y.F.ZHOU,L.F.LI,Y.H.LIANG,X.-D.SU JRNL TITL CRYSTAL STRUCTURES OF YTBE AND YVGN FROM BACILUS JRNL TITL 2 SUBTILIS REVEAL A NEW ALDO-KETO REDUCTASE FAMILY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 52232 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2780 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3753 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 205 REMARK 3 BIN FREE R VALUE : 0.3590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS : 4781 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.74000 REMARK 3 B22 (A**2) : -1.91000 REMARK 3 B33 (A**2) : -0.83000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.152 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.688 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4550 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6143 ; 1.821 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 550 ; 6.391 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 222 ;37.559 ;25.405 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 836 ;17.447 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;26.084 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 671 ; 0.224 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3438 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1969 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2989 ; 0.294 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 228 ; 0.162 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 30 ; 0.290 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.417 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2763 ; 0.936 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4417 ; 1.512 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1862 ; 2.599 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1726 ; 3.918 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 276 6 REMARK 3 1 B 1 B 276 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 A (A): 2197 ; 0.360 ; 5.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 2197 ; 1.020 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 276 REMARK 3 ORIGIN FOR THE GROUP (A): -17.8190 10.3070 -22.3170 REMARK 3 T TENSOR REMARK 3 T11: -0.0914 T22: -0.1018 REMARK 3 T33: -0.0876 T12: 0.0194 REMARK 3 T13: -0.0049 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.3468 L22: 2.8651 REMARK 3 L33: 2.1161 L12: 0.0926 REMARK 3 L13: -0.1198 L23: 0.8999 REMARK 3 S TENSOR REMARK 3 S11: -0.0383 S12: -0.0370 S13: 0.0075 REMARK 3 S21: -0.2401 S22: -0.0367 S23: 0.0529 REMARK 3 S31: 0.1559 S32: -0.0169 S33: 0.0750 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 276 REMARK 3 ORIGIN FOR THE GROUP (A): -18.3870 41.9870 -6.5750 REMARK 3 T TENSOR REMARK 3 T11: -0.0356 T22: -0.1122 REMARK 3 T33: -0.0918 T12: -0.0057 REMARK 3 T13: 0.0061 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 0.3142 L22: 2.5292 REMARK 3 L33: 1.9589 L12: -0.2158 REMARK 3 L13: 0.1158 L23: 1.1392 REMARK 3 S TENSOR REMARK 3 S11: 0.0159 S12: -0.0184 S13: 0.0209 REMARK 3 S21: -0.2316 S22: -0.0431 S23: 0.0108 REMARK 3 S31: -0.2090 S32: 0.0066 S33: 0.0272 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 3B3E COMPLIES WITH FORMAT V. 3.1, 01-AUG-2007 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE RCSB ID CODE IS RCSB045028. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74192 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.623 REMARK 200 RESOLUTION RANGE LOW (A) : 125.046 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.26400 REMARK 200 R SYM (I) : 0.26400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 1.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.01400 REMARK 200 R SYM FOR SHELL (I) : 1.42200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 7.5, 0.4M SODIUM REMARK 280 NITRATE, 40% PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 1/2-X,1/2+Y,-Z REMARK 290 4555 1/2+X,1/2-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 40.31650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 62.52300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.31650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 62.52300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSEQI REMARK 465 MET A -33 REMARK 465 GLY A -32 REMARK 465 SER A -31 REMARK 465 SER A -30 REMARK 465 HIS A -29 REMARK 465 HIS A -28 REMARK 465 HIS A -27 REMARK 465 HIS A -26 REMARK 465 HIS A -25 REMARK 465 HIS A -24 REMARK 465 SER A -23 REMARK 465 SER A -22 REMARK 465 GLY A -21 REMARK 465 LEU A -20 REMARK 465 VAL A -19 REMARK 465 PRO A -18 REMARK 465 ARG A -17 REMARK 465 GLY A -16 REMARK 465 SER A -15 REMARK 465 HIS A -14 REMARK 465 MET A -13 REMARK 465 ALA A -12 REMARK 465 SER A -11 REMARK 465 MET A -10 REMARK 465 THR A -9 REMARK 465 GLY A -8 REMARK 465 GLY A -7 REMARK 465 GLN A -6 REMARK 465 GLN A -5 REMARK 465 MET A -4 REMARK 465 GLY A -3 REMARK 465 ARG A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET B -33 REMARK 465 GLY B -32 REMARK 465 SER B -31 REMARK 465 SER B -30 REMARK 465 HIS B -29 REMARK 465 HIS B -28 REMARK 465 HIS B -27 REMARK 465 HIS B -26 REMARK 465 HIS B -25 REMARK 465 HIS B -24 REMARK 465 SER B -23 REMARK 465 SER B -22 REMARK 465 GLY B -21 REMARK 465 LEU B -20 REMARK 465 VAL B -19 REMARK 465 PRO B -18 REMARK 465 ARG B -17 REMARK 465 GLY B -16 REMARK 465 SER B -15 REMARK 465 HIS B -14 REMARK 465 MET B -13 REMARK 465 ALA B -12 REMARK 465 SER B -11 REMARK 465 MET B -10 REMARK 465 THR B -9 REMARK 465 GLY B -8 REMARK 465 GLY B -7 REMARK 465 GLN B -6 REMARK 465 GLN B -5 REMARK 465 MET B -4 REMARK 465 GLY B -3 REMARK 465 ARG B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU B 201 CG CD OE1 OE2 REMARK 470 LYS B 235 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 NH2 ARG B 100 O HOH B 353 2.11 REMARK 500 O HOH A 378 O HOH A 398 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 VAL A 228 CB VAL A 228 CG2 0.127 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 VAL A 140 CG1 - CB - CG2 ANGL. DEV. = 10.7 DEGREES REMARK 500 VAL A 140 CA - CB - CG1 ANGL. DEV. = 9.8 DEGREES REMARK 500 LEU A 170 CA - CB - CG ANGL. DEV. = 15.2 DEGREES REMARK 500 ARG B 176 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 26 18.98 57.81 REMARK 500 LYS A 116 -60.21 -100.63 REMARK 500 ASP A 117 29.30 -156.54 REMARK 500 LYS A 263 20.75 -141.49 REMARK 500 PRO B 2 155.56 -49.69 REMARK 500 LYS B 26 28.25 48.26 REMARK 500 ASN B 29 163.09 154.16 REMARK 500 LYS B 116 -63.78 -95.15 REMARK 500 ASP B 117 33.22 -151.02 REMARK 500 ASP B 264 46.77 34.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU B 28 ASN B 29 -149.56 REMARK 500 ASN B 29 GLY B 30 139.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,A12) REMARK 500 REMARK 500 M RES CSSEQI OMEGA REMARK 500 ASN B 29 ALPHA-CARBON 122.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 277 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 277 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 278 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 278 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 279 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 279 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 280 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3B3D RELATED DB: PDB REMARK 900 YTBE DBREF 3B3E A 1 276 UNP O32210 O32210_BACSU 1 276 DBREF 3B3E B 1 276 UNP O32210 O32210_BACSU 1 276 SEQADV 3B3E MET A -33 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY A -32 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER A -31 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER A -30 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS A -29 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS A -28 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS A -27 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS A -26 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS A -25 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS A -24 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER A -23 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER A -22 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY A -21 UNP O32210 EXPRESSION TAG SEQADV 3B3E LEU A -20 UNP O32210 EXPRESSION TAG SEQADV 3B3E VAL A -19 UNP O32210 EXPRESSION TAG SEQADV 3B3E PRO A -18 UNP O32210 EXPRESSION TAG SEQADV 3B3E ARG A -17 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY A -16 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER A -15 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS A -14 UNP O32210 EXPRESSION TAG SEQADV 3B3E MET A -13 UNP O32210 EXPRESSION TAG SEQADV 3B3E ALA A -12 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER A -11 UNP O32210 EXPRESSION TAG SEQADV 3B3E MET A -10 UNP O32210 EXPRESSION TAG SEQADV 3B3E THR A -9 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY A -8 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY A -7 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLN A -6 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLN A -5 UNP O32210 EXPRESSION TAG SEQADV 3B3E MET A -4 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY A -3 UNP O32210 EXPRESSION TAG SEQADV 3B3E ARG A -2 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY A -1 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER A 0 UNP O32210 EXPRESSION TAG SEQADV 3B3E MET B -33 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY B -32 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER B -31 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER B -30 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS B -29 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS B -28 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS B -27 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS B -26 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS B -25 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS B -24 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER B -23 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER B -22 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY B -21 UNP O32210 EXPRESSION TAG SEQADV 3B3E LEU B -20 UNP O32210 EXPRESSION TAG SEQADV 3B3E VAL B -19 UNP O32210 EXPRESSION TAG SEQADV 3B3E PRO B -18 UNP O32210 EXPRESSION TAG SEQADV 3B3E ARG B -17 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY B -16 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER B -15 UNP O32210 EXPRESSION TAG SEQADV 3B3E HIS B -14 UNP O32210 EXPRESSION TAG SEQADV 3B3E MET B -13 UNP O32210 EXPRESSION TAG SEQADV 3B3E ALA B -12 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER B -11 UNP O32210 EXPRESSION TAG SEQADV 3B3E MET B -10 UNP O32210 EXPRESSION TAG SEQADV 3B3E THR B -9 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY B -8 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY B -7 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLN B -6 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLN B -5 UNP O32210 EXPRESSION TAG SEQADV 3B3E MET B -4 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY B -3 UNP O32210 EXPRESSION TAG SEQADV 3B3E ARG B -2 UNP O32210 EXPRESSION TAG SEQADV 3B3E GLY B -1 UNP O32210 EXPRESSION TAG SEQADV 3B3E SER B 0 UNP O32210 EXPRESSION TAG SEQRES 1 A 310 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 310 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 A 310 GLY GLN GLN MET GLY ARG GLY SER MET PRO THR SER LEU SEQRES 4 A 310 LYS ASP THR VAL LYS LEU HIS ASN GLY VAL GLU MET PRO SEQRES 5 A 310 TRP PHE GLY LEU GLY VAL PHE LYS VAL GLU ASN GLY ASN SEQRES 6 A 310 GLU ALA THR GLU SER VAL LYS ALA ALA ILE LYS ASN GLY SEQRES 7 A 310 TYR ARG SER ILE ASP THR ALA ALA ILE TYR LYS ASN GLU SEQRES 8 A 310 GLU GLY VAL GLY ILE GLY ILE LYS GLU SER GLY VAL ALA SEQRES 9 A 310 ARG GLU GLU LEU PHE ILE THR SER LYS VAL TRP ASN GLU SEQRES 10 A 310 ASP GLN GLY TYR GLU THR THR LEU ALA ALA PHE GLU LYS SEQRES 11 A 310 SER LEU GLU ARG LEU GLN LEU ASP TYR LEU ASP LEU TYR SEQRES 12 A 310 LEU ILE HIS TRP PRO GLY LYS ASP LYS TYR LYS ASP THR SEQRES 13 A 310 TRP ARG ALA LEU GLU LYS LEU TYR LYS ASP GLY LYS ILE SEQRES 14 A 310 ARG ALA ILE GLY VAL SER ASN PHE GLN VAL HIS HIS LEU SEQRES 15 A 310 GLU GLU LEU LEU LYS ASP ALA GLU ILE LYS PRO MET VAL SEQRES 16 A 310 ASN GLN VAL GLU PHE HIS PRO ARG LEU THR GLN LYS GLU SEQRES 17 A 310 LEU ARG ASP TYR CYS LYS GLY GLN GLY ILE GLN LEU GLU SEQRES 18 A 310 ALA TRP SER PRO LEU MET GLN GLY GLN LEU LEU ASP ASN SEQRES 19 A 310 GLU VAL LEU THR GLN ILE ALA GLU LYS HIS ASN LYS SER SEQRES 20 A 310 VAL ALA GLN VAL ILE LEU ARG TRP ASP LEU GLN HIS GLY SEQRES 21 A 310 VAL VAL THR ILE PRO LYS SER ILE LYS GLU HIS ARG ILE SEQRES 22 A 310 ILE GLU ASN ALA ASP ILE PHE ASP PHE GLU LEU SER GLN SEQRES 23 A 310 GLU ASP MET ASP LYS ILE ASP ALA LEU ASN LYS ASP GLU SEQRES 24 A 310 ARG VAL GLY PRO ASN PRO ASP GLU LEU LEU PHE SEQRES 1 B 310 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 310 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 B 310 GLY GLN GLN MET GLY ARG GLY SER MET PRO THR SER LEU SEQRES 4 B 310 LYS ASP THR VAL LYS LEU HIS ASN GLY VAL GLU MET PRO SEQRES 5 B 310 TRP PHE GLY LEU GLY VAL PHE LYS VAL GLU ASN GLY ASN SEQRES 6 B 310 GLU ALA THR GLU SER VAL LYS ALA ALA ILE LYS ASN GLY SEQRES 7 B 310 TYR ARG SER ILE ASP THR ALA ALA ILE TYR LYS ASN GLU SEQRES 8 B 310 GLU GLY VAL GLY ILE GLY ILE LYS GLU SER GLY VAL ALA SEQRES 9 B 310 ARG GLU GLU LEU PHE ILE THR SER LYS VAL TRP ASN GLU SEQRES 10 B 310 ASP GLN GLY TYR GLU THR THR LEU ALA ALA PHE GLU LYS SEQRES 11 B 310 SER LEU GLU ARG LEU GLN LEU ASP TYR LEU ASP LEU TYR SEQRES 12 B 310 LEU ILE HIS TRP PRO GLY LYS ASP LYS TYR LYS ASP THR SEQRES 13 B 310 TRP ARG ALA LEU GLU LYS LEU TYR LYS ASP GLY LYS ILE SEQRES 14 B 310 ARG ALA ILE GLY VAL SER ASN PHE GLN VAL HIS HIS LEU SEQRES 15 B 310 GLU GLU LEU LEU LYS ASP ALA GLU ILE LYS PRO MET VAL SEQRES 16 B 310 ASN GLN VAL GLU PHE HIS PRO ARG LEU THR GLN LYS GLU SEQRES 17 B 310 LEU ARG ASP TYR CYS LYS GLY GLN GLY ILE GLN LEU GLU SEQRES 18 B 310 ALA TRP SER PRO LEU MET GLN GLY GLN LEU LEU ASP ASN SEQRES 19 B 310 GLU VAL LEU THR GLN ILE ALA GLU LYS HIS ASN LYS SER SEQRES 20 B 310 VAL ALA GLN VAL ILE LEU ARG TRP ASP LEU GLN HIS GLY SEQRES 21 B 310 VAL VAL THR ILE PRO LYS SER ILE LYS GLU HIS ARG ILE SEQRES 22 B 310 ILE GLU ASN ALA ASP ILE PHE ASP PHE GLU LEU SER GLN SEQRES 23 B 310 GLU ASP MET ASP LYS ILE ASP ALA LEU ASN LYS ASP GLU SEQRES 24 B 310 ARG VAL GLY PRO ASN PRO ASP GLU LEU LEU PHE HET NO3 A 277 4 HET NO3 A 278 4 HET NO3 A 279 4 HET NO3 B 277 4 HET NO3 B 278 4 HET NO3 B 279 4 HET NO3 B 280 4 HETNAM NO3 NITRATE ION FORMUL 3 NO3 7(N O3 1-) FORMUL 10 HOH *281(H2 O) HELIX 1 1 GLY A 30 ASN A 43 1 14 HELIX 2 2 ALA A 51 LYS A 55 5 5 HELIX 3 3 ASN A 56 SER A 67 1 12 HELIX 4 4 ALA A 70 LEU A 74 5 5 HELIX 5 5 TRP A 81 GLN A 85 5 5 HELIX 6 6 GLY A 86 GLN A 102 1 17 HELIX 7 7 LYS A 118 ASP A 132 1 15 HELIX 8 8 GLN A 144 ALA A 155 1 12 HELIX 9 9 GLN A 172 GLY A 183 1 12 HELIX 10 10 LEU A 192 GLN A 196 5 5 HELIX 11 11 ASN A 200 ASN A 211 1 12 HELIX 12 12 SER A 213 HIS A 225 1 13 HELIX 13 13 LYS A 235 ALA A 243 1 9 HELIX 14 14 SER A 251 ALA A 260 1 10 HELIX 15 15 GLY B 30 ASN B 43 1 14 HELIX 16 16 ALA B 51 LYS B 55 5 5 HELIX 17 17 ASN B 56 SER B 67 1 12 HELIX 18 18 ALA B 70 LEU B 74 5 5 HELIX 19 19 TRP B 81 GLN B 85 5 5 HELIX 20 20 GLY B 86 GLN B 102 1 17 HELIX 21 21 LYS B 118 ASP B 132 1 15 HELIX 22 22 GLN B 144 ALA B 155 1 12 HELIX 23 23 GLN B 172 GLY B 183 1 12 HELIX 24 24 LEU B 192 GLN B 196 5 5 HELIX 25 25 ASN B 200 ASN B 211 1 12 HELIX 26 26 SER B 213 HIS B 225 1 13 HELIX 27 27 LYS B 235 ASP B 244 1 10 HELIX 28 28 SER B 251 ALA B 260 1 10 SHEET 1 A 2 THR A 8 LYS A 10 0 SHEET 2 A 2 GLU A 16 PRO A 18 -1 O MET A 17 N VAL A 9 SHEET 1 B 8 LEU A 22 GLY A 23 0 SHEET 2 B 8 SER A 47 ASP A 49 1 O ASP A 49 N LEU A 22 SHEET 3 B 8 PHE A 75 VAL A 80 1 O PHE A 75 N ILE A 48 SHEET 4 B 8 LEU A 106 ILE A 111 1 O LEU A 110 N VAL A 80 SHEET 5 B 8 ILE A 135 SER A 141 1 O SER A 141 N ILE A 111 SHEET 6 B 8 VAL A 161 GLU A 165 1 O VAL A 161 N VAL A 140 SHEET 7 B 8 GLN A 185 TRP A 189 1 O TRP A 189 N VAL A 164 SHEET 8 B 8 VAL A 228 THR A 229 1 O VAL A 228 N ALA A 188 SHEET 1 C 2 THR B 8 LYS B 10 0 SHEET 2 C 2 GLU B 16 PRO B 18 -1 O MET B 17 N VAL B 9 SHEET 1 D 8 LEU B 22 GLY B 23 0 SHEET 2 D 8 SER B 47 ASP B 49 1 O ASP B 49 N LEU B 22 SHEET 3 D 8 PHE B 75 VAL B 80 1 O PHE B 75 N ILE B 48 SHEET 4 D 8 LEU B 106 ILE B 111 1 O LEU B 110 N VAL B 80 SHEET 5 D 8 ILE B 135 SER B 141 1 O GLY B 139 N TYR B 109 SHEET 6 D 8 VAL B 161 GLU B 165 1 O VAL B 161 N VAL B 140 SHEET 7 D 8 GLN B 185 TRP B 189 1 O GLU B 187 N VAL B 164 SHEET 8 D 8 VAL B 228 THR B 229 1 O VAL B 228 N ALA B 188 SITE 1 AC1 8 PHE A 25 SER A 190 PRO A 191 LEU A 192 SITE 2 AC1 8 MET A 193 GLN A 194 PRO A 231 LYS A 232 SITE 1 AC2 8 PHE B 25 SER B 190 PRO B 191 LEU B 192 SITE 2 AC2 8 MET B 193 GLN B 194 PRO B 231 LYS B 232 SITE 1 AC3 7 LEU A 192 GLY A 195 LEU A 198 VAL A 214 SITE 2 AC3 7 ARG A 238 HOH A 302 HOH A 329 SITE 1 AC4 7 LEU B 192 GLY B 195 LEU B 198 ARG B 238 SITE 2 AC4 7 HOH B 295 HOH B 301 HOH B 395 SITE 1 AC5 5 ASP B 117 LYS B 118 TYR B 119 LYS B 120 SITE 2 AC5 5 ASP B 121 SITE 1 AC6 5 ASP A 117 LYS A 118 TYR A 119 LYS A 120 SITE 2 AC6 5 ASP A 121 SITE 1 AC7 8 LYS A 55 HOH A 356 ALA B 52 LYS B 55 SITE 2 AC7 8 ARG B 100 HOH B 307 HOH B 334 HOH B 421 CRYST1 80.633 125.046 57.859 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012402 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007997 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017283 0.00000